ArticleNature communications2024
A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 11 citations in OpenAlex.
- Muscle-specific CUT&Tag profiling dataset of UNC-130 in Caenorhabditis elegans.BMC genomic data · 2026Article
- Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE.bioRxiv : the preprint server for biology · 2025Article
- Stereotyped Subclones Revealed by High-Density Single-Cell Lineage Tracing Support Robust Development.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A dataset of expression profile of certain microRNAs in Caenorhabditis elegans.Scientific data · 2025Article
- Automated segmentation and recognition of C. elegans whole-body cells.Bioinformatics (Oxford, England) · 2024Article
- A lineage-resolved cartography of microRNA promoter activity in C. elegans empowers multidimensional developmental analysis.Nature communications · 2024Article
- A full-body transcription factor expression atlas with completely resolved cell identities in C. elegans.Nature communications · 2024Article
- Tissue-specific silencing of integrated transgenes achieved through endogenous RNA interference inRNA biology · 2024Article
Corrections and comments
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Authors and funding
10 authors at 5 institutions in 2 countries.
Funding
Abstract
Invariant cell lineage in C. elegans enables spatiotemporal resolution of transcriptional regulatory mechanisms controlling the fate of each cell. Here, we develop RAPCAT (Robust-point-matching- And Piecewise-affine-based Cell Annotation Tool) to automate cell identity assignment in three-dimensional image stacks of L1 larvae and profile reporter expression of 620 transcription factors in every cell. Transcription factor profile-based clustering analysis defines 80 cell types distinct from conventional phenotypic cell types and identifies three general phenotypic modalities related to these classifications. First, transcription factors are broadly downregulated in quiescent stage Hermaphrodite Specific Neurons, suggesting stage- and cell type-specific variation in transcriptome size. Second, transcription factor expression is more closely associated with morphology than other phenotypic modalities in different pre- and post-differentiation developmental stages. Finally, embryonic cell lineages can be associated with specific transcription factor expression patterns and functions that persist throughout postembryonic life. This study presents a comprehensive transcription factor atlas for investigation of intra-cell type heterogeneity.
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